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Crystal structure of spectinomycin adenyltransferase AAD(9) from Enterococcus faecialis with ATP and spectinomycin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SXJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 281 10% w/v PEG 4000, 20% v/v glycerol, 0.02 M of each monosaccharide (0.2 M D-glucose, 0.2 M D-mannose, 0.2 M D-galactose, 0.2 M L-fucose, 0.2 M D-xylose, 0.2 M N-acetyl-D-glucosamine), 0.1 M MOPS/HEPES-Na pH 7.5 and soaked with 10 mM ATP, 10 mM MgCl2 and pinch of spectinomycin powder
Crystal Properties Matthews coefficient Solvent content 2.5 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.532 α = 90 b = 69.312 β = 135 c = 94.517 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 XE 16M 2019-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97950 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 3 55.9 99.8 0.2 0.3 0.9 5.4 6.3 12346 48.46
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.1 99.9 1.3 0.5 1.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6SXJ 3 55.89 1.34 12341 623 99.87 0.2411 0.2397 0.2421 0.2711 0.2751 44.06
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 2.5658 f_angle_d 0.5119 f_chiral_restr 0.0375 f_plane_restr 0.0033 f_bond_d 0.0022
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4062 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms 113
Software Software Software Name Purpose XDS data reduction PHENIX refinement XDS data reduction Aimless data scaling Coot model building PHASER phasing XDS data reduction